I have removed the list of points previously posted because I have found a new set of arguments that I think completely answers all of the conspiracy points.
These arguments are presented more fully in the excellent book:.
JFK: The Smoking Gun, by Colin McLaren
The main takeaways from this conspiracy explanation are:
1) Lee Harvey Oswald, in the School Book Depository, did shoot and hit President Kennedy and Governor Connally. Oswald was firing full metal jacket bullets which are designed to stay whole and pass through the body. They are battlefield weapons designed to get a soldier out of the battlefield and not inflict catastrophic injuries. Note, these bullets do not explode when they go into the body. they just pass through. The kill shot, as seen in the Zappruder film, the exploding head shot, was a different kind of bullet to the ones Oswald was using. The head shot wound was caused by a frangible bullet. So there must have been a second shooter.
2) The second shot came from behind, but not from the school book depository. A number of witnesses on the ground say they could smell gunshot - the school book depository window was too far away to allow witnesses on the road to smell anything so the smell must have come from somewhere else, closer.
3) Kennedy's fatal head shot came from behind. The bullet wound behind Kennedy's neck is an entrance wound. The frangible, exploding, bullet, was an accidental shot from a security officer traveling in the car behind the president. The book names this individual which we will not do even though he has now died. The essence of what happened was that the car jolted, the shooter lost his balance and fired accidentally. It was a horrible, terrible, nightmare of an accident. The shot hit the president in the head killing him instantly. The semi automatic weapons being used by the security detail in the car behind were new. They were suspended from use for a period after the incident.
4) If one of the security detail, traveling in the car behind, shot the president this also explains the cover-up. It explains the care taken to see what the Zappruder film actually showed and then keeping it under wraps for years. The pictures taken by witnesses at the scene were all taken. The control of the autopsy to make sure no evidence of an FBI shot was ever reported.